Allele Frequencies

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chr (2): region, chr
dbl (3): midPos, Nsites, Fst
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This next set of figures were made using ANGSD Allele Frequency estimation. This was run with a known major and unknown minor, in which the unknown minor allele frequency is plotted on the y-axis. The major allele is assumed to be known (inferred or given by user) however the minor allele is not determined. Instead it is summed over the 3 possible minor alleles weighted by their probabilities. The allele frequency estimator from genotype likelihoods was done using the EM algorithm. Targeting chromosome 3, and further the specific region around 24,700,000 bp, was chosen based on the pairwise Fst sliding window plot above, where we see a spike at chromosome 3 in that particular region interesting in that previous studies found an average Fst of 0.008 when comparing Canadian to Southern New England or Mid-Atlantic samples, making the Fst values in this region magnitudes larger than expected. The last time the lab (Anthony) saw a peak such as this, it was the greb1l gene. All ANGSD runs also were referenced to the American shad genome.

The following figure is constrained on chromosome 3 to region 24,704,000-24,750,000.

The following figure shows the allele frequencies on a broader range on chromosome 3 from 24,650,000-24,780,000 with a minimum minor allele frequency of 0.05.

The following figure is similar to the previous, but contains all minor allele frequencies.

GRL:

The following two figures are the minor allele frequencies from only the Great Lakes and Finger Lakes samples, with the first being unfiltered for minimum allele frequency and the second having a minMaf of 0.05.

SANAD:

The following two figures are the minor allele frequencies from only the South Atlantic Gulf and Mid-Atlantic samples, with the first being unfiltered for minimum allele frequency and the second having a minMaf of 0.05.

NANAD:

The following two figures are the minor allele frequencies from only the Canadian and Northern New England samples, with the first being unfiltered for minimum allele frequency and the second having a minMaf of 0.05.

Screen grab from UCSC genome browser of American shad reference genome at our region of interest as found in the pairwise Fst plot.

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chr (4): Gene, Official Full Name, Gene Type, Su...
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Genes Within The Region of Interest
chr3:24,660,000-24,750,000
	Official Full Name	Gene Type	Summary
pvalb4	parvalbumin 4	protein coding	predicted to enable calcium ion binding activity
			predicted to be activate in cytoplasm and nucleus
			is expressed in musculature system; myotome; and pectoral fin muscle
pvalb8	parvalbumin 8	protein coding	predicted to enable calcium ion binding activity
			predicted to be active in cytoplasm and nucleus
			is expressed in several structures, including adenohypophyseal placode; epidermal cell; hypophysis; integument; and sensory system
			othologous to several human genes including OCM2
lmtk2	lemur tyrosine kinase 2	protein coding	predicted to enable ATP binding activity and protein kinase activity
			predicted to be involved in axogenesis; positive regulation of kinase activity; and transmembrane receptor protein tyrosine kinase signaling pathway
			predicted to act upstream of or within protein phosphorylation
			predicted to be part of receptor complex
			predicted to be integral component of plasma membrane
			orthologous to human LMTK2
aimp2	aminoacyl tRNA synthetase complex interacting multifunctional protein 2	protein coding	predicted to be involved in positive regulation of aminoacyl-tRNA ligase activity
			predicted to act upstream of or within apoptotic process and cell differentiation
			predicted to be located in cytodol and nucleus
			predicted to be part of aminoacyl-tRNA synthetase multienzyme complex
			is expressed in several structures, including alar plate midbrain region; head; immature eye; midbrain; and musculature system
			human ortholog of this gene implicated in hypomyelinating leukodystrophy, a group of neurodevelopmental disorders that affect proper formation of the myelin sheath in the central nervous system
myl7	myosin, light chain 7, regulatory	protein coding	predicted to enable calcium ion binding activity
			acts upstream of or within several processes, including cardiac muscle cell proliferationl heart contraction; and myofibril assembly
			is expressed in several structures, including corpsucles of Stannis; heart primordium; mesoderm; muscle; and pericardial region
			orthologous to human MYL7
cacng4b	calcium channel, voltage-dependent, gamma subunit 4b	protein coding	predicted to enable channel regulator activity and voltage-gated calcium channel activity
			predicted to be involved in serveal processes, including neurotransmitter receptor internalization; neurotransmitter receptor transport, postsynaptic endosome to lysosome; and postsynaptic neurotransmitter receptor diffusion trapping
			predicted to act upstream of or within calcium ion transmembrane transport and regulation of ion transmembrane transport
			predicted to be located in membrane
			predicted to be integral component of membrane
			predicted to be part of AMPA glutamate receptor complex
			predicted to be active in postsynaptic density membrane
			orthologous to human CACNG4
cacng1b	calcium channel, voltage-dependent, gamma subunit 1b	protein coding	predicted to enable calcium channel regulator activity
			predicted to be involved in regulation of calcium ion transmembrane transport via high voltage-gated calcium channel
			predicted to act upstream of or within calcium ion transmembrane transport and regulation of ion transmembrane transport
			predicted to be located in plasma membrane
			predicted to be integral component of membrane
			predicted to be part of L-type voltage-gated calcium channel complex
			human ortholog(s) of this gene implicated in malignant hyperthermia, a severe reaction to certain drugs used for anesthesia with fast rise in body temperature, rigid muscles or spasms, and rapid heart rate
References
pvalb4: https://www.ncbi.nlm.nih.gov/gene/?term=Danio+rerio+pvalb4
pvalb8: https://www.ncbi.nlm.nih.gov/gene/?term=Danio+rerio+pvalb8
lmtk2: https://www.ncbi.nlm.nih.gov/gene/564666/
aimp2: https://www.ncbi.nlm.nih.gov/gene/406647
myl7: https://www.ncbi.nlm.nih.gov/gene/30592/
cacng4b: https://www.ncbi.nlm.nih.gov/gene/794222/
cacng1b: https://www.ncbi.nlm.nih.gov/gene/571193